[English] 日本語
Yorodumi
- PDB-6i0z: CRYSTAL STRUCTURE OF FASCIN IN COMPLEX WITH COMPOUND 1 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6i0z
TitleCRYSTAL STRUCTURE OF FASCIN IN COMPLEX WITH COMPOUND 1
ComponentsFascin
KeywordsSTRUCTURAL PROTEIN / actin bundling / small molecule inhibition
Function / homology
Function and homology information


microspike / parallel actin filament bundle assembly / regulation of microvillus assembly / positive regulation of extracellular matrix disassembly / establishment of apical/basal cell polarity / microspike assembly / cell projection membrane / cell-cell junction assembly / positive regulation of podosome assembly / positive regulation of filopodium assembly ...microspike / parallel actin filament bundle assembly / regulation of microvillus assembly / positive regulation of extracellular matrix disassembly / establishment of apical/basal cell polarity / microspike assembly / cell projection membrane / cell-cell junction assembly / positive regulation of podosome assembly / positive regulation of filopodium assembly / podosome / microvillus / establishment or maintenance of cell polarity / actin filament bundle assembly / positive regulation of lamellipodium assembly / stress fiber / ruffle / regulation of actin cytoskeleton organization / filopodium / cell motility / actin filament binding / cell-cell junction / cell migration / lamellipodium / actin cytoskeleton / growth cone / actin binding / actin cytoskeleton organization / Interleukin-4 and Interleukin-13 signaling / cell cortex / protein-macromolecule adaptor activity / cytoskeleton / cadherin binding / RNA binding / extracellular exosome / cytosol / cytoplasm
Similarity search - Function
Fascin / Fascin, metazoans / Fascin domain / Fascin domain / Actin-crosslinking / Trefoil (Acidic Fibroblast Growth Factor, subunit A) - #50 / Trefoil (Acidic Fibroblast Growth Factor, subunit A) / Trefoil / Mainly Beta
Similarity search - Domain/homology
~{N}-(2,4-dichlorophenyl)-~{N}-methyl-ethanamide / Fascin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.77 Å
AuthorsSchuettelkopf, A.W.
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2019
Title: Structure-based design, synthesis and biological evaluation of a novel series of isoquinolone and pyrazolo[4,3-c]pyridine inhibitors of fascin 1 as potential anti-metastatic agents.
Authors: Francis, S. / Croft, D. / Schuttelkopf, A.W. / Parry, C. / Pugliese, A. / Cameron, K. / Claydon, S. / Drysdale, M. / Gardner, C. / Gohlke, A. / Goodwin, G. / Gray, C.H. / Konczal, J. / ...Authors: Francis, S. / Croft, D. / Schuttelkopf, A.W. / Parry, C. / Pugliese, A. / Cameron, K. / Claydon, S. / Drysdale, M. / Gardner, C. / Gohlke, A. / Goodwin, G. / Gray, C.H. / Konczal, J. / McDonald, L. / Mezna, M. / Pannifer, A. / Paul, N.R. / Machesky, L. / McKinnon, H. / Bower, J.
History
DepositionOct 27, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 27, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2019Group: Data collection / Database references / Category: citation / pdbx_database_proc
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jan 24, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Fascin
B: Fascin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,6404
Polymers109,2042
Non-polymers4362
Water10,575587
1
A: Fascin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,8202
Polymers54,6021
Non-polymers2181
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Fascin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,8202
Polymers54,6021
Non-polymers2181
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)159.910, 71.620, 113.320
Angle α, β, γ (deg.)90.000, 130.900, 90.000
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein Fascin / 55 kDa actin-bundling protein / Singed-like protein / p55


Mass: 54601.879 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FSCN1, FAN1, HSN, SNL / Plasmid: pBDDP-SPR3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) pLysS / References: UniProt: Q16658
#2: Chemical ChemComp-GZQ / ~{N}-(2,4-dichlorophenyl)-~{N}-methyl-ethanamide


Mass: 218.080 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H9Cl2NO / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 587 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.25 Å3/Da / Density % sol: 45.23 % / Mosaicity: 0.204 °
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / Details: 16-20% PEG 3350, 200 mM LiAc, 4% glycerol

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 1.0781 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 8, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0781 Å / Relative weight: 1
ReflectionResolution: 1.77→36.72 Å / Num. obs: 93872 / % possible obs: 99.5 % / Redundancy: 3.7 % / Biso Wilson estimate: 23.131 Å2 / Rmerge(I) obs: 0.045 / Rpim(I) all: 0.034 / Rrim(I) all: 0.065 / Net I/σ(I): 16
Reflection shellResolution: 1.77→1.82 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.535 / Mean I/σ(I) obs: 2.3 / Rpim(I) all: 0.365 / Rrim(I) all: 0.709 / % possible all: 99.9

-
Processing

Software
NameVersionClassification
REFMAC5.8.0222refinement
xia20.3.4.0data scaling
PDB_EXTRACT3.22data extraction
xia20.3.4.0data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3P53

3p53


Resolution: 1.77→36.72 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.937 / SU B: 8.644 / SU ML: 0.115 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.135 / ESU R Free: 0.124
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2268 4705 5 %RANDOM
Rwork0.1949 ---
obs0.1965 89166 99.45 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 92.7 Å2 / Biso mean: 39.067 Å2 / Biso min: 23.05 Å2
Baniso -1Baniso -2Baniso -3
1--0.1 Å20 Å21.74 Å2
2---5.02 Å20 Å2
3---0.85 Å2
Refinement stepCycle: final / Resolution: 1.77→36.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7555 0 26 587 8168
Biso mean--36.21 44.05 -
Num. residues----967
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0147813
X-RAY DIFFRACTIONr_bond_other_d0.0010.0176788
X-RAY DIFFRACTIONr_angle_refined_deg1.6131.66110572
X-RAY DIFFRACTIONr_angle_other_deg1.6011.64815922
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1115977
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.37421.377443
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.709151285
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.0931566
X-RAY DIFFRACTIONr_chiral_restr0.0990.21004
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.029016
X-RAY DIFFRACTIONr_gen_planes_other0.0110.021528
X-RAY DIFFRACTIONr_mcbond_it0.6650.7883908
X-RAY DIFFRACTIONr_mcbond_other0.6650.7883907
X-RAY DIFFRACTIONr_mcangle_it1.0861.1784887
LS refinement shellResolution: 1.77→1.816 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.286 317 -
Rwork0.279 6618 -
all-6935 -
obs--99.84 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.48310.8641-0.02964.80850.30761.7690.0228-0.0577-0.2112-0.045-0.1301-0.47680.10960.17010.10730.342-0.0112-0.04880.40780.0380.165736.87327.65324.128
21.56390.1682-0.05332.9946-0.55852.10250.0807-0.11670.10480.2173-0.05680.1463-0.17730.0309-0.02390.3807-0.0203-0.08340.3883-0.01480.040516.2518.25337.119
31.576-1.58140.37563.27220.7732.1946-0.0209-0.2016-0.15590.248-0.00340.09750.2590.11480.02430.41490.0229-0.05390.4190.02090.088523.076-12.56537.129
41.64050.36340.05863.77920.3463.76920.05960.20650.0313-0.2531-0.0292-0.1312-0.15760.2349-0.03030.35160.0415-0.08360.3925-0.01690.034222.0660.22214.795
51.48470.11350.52643.6527-1.2354.4467-0.0998-0.0017-0.11950.03340.07690.04360.06010.00920.02290.3480.029-0.07230.37690.04220.072258.1089.2270.537
61.7118-1.09370.35383.3045-0.12021.6291-0.0553-0.0730.12860.160.0024-0.2412-0.30180.01380.05290.3865-0.0092-0.09350.35690.01060.08372.7991.55920.758
73.9437-0.23610.24083.09280.53611.8668-0.00170.1308-0.7859-0.0466-0.0197-0.01020.34090.08570.02150.3390.0014-0.08030.3308-0.01880.231371.713-30.36318.803
84.7323-0.0752-0.2192.898-0.34652.2951-0.00950.07990.145-0.0006-0.01010.4121-0.091-0.35760.01960.3116-0.0031-0.09730.396-0.00030.162650.15-1619.573
90.3459-0.0841-0.07010.0390.03030.02540.02230.02570.00010.0207-0.0237-0.0095-0.0115-0.00480.00140.5216-0.0007-0.10340.52430.00510.185742.8244.01221.869
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A6 - 138
2X-RAY DIFFRACTION2A139 - 260
3X-RAY DIFFRACTION3A261 - 384
4X-RAY DIFFRACTION4A385 - 493
5X-RAY DIFFRACTION5B6 - 138
6X-RAY DIFFRACTION6B139 - 260
7X-RAY DIFFRACTION7B261 - 384
8X-RAY DIFFRACTION8B385 - 493
9X-RAY DIFFRACTION9A501
10X-RAY DIFFRACTION9A601 - 868

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more